1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
|
#include <ctype.h>
#include "bam.h"
#include "khash.h"
typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
KHASH_MAP_INIT_STR(r2l, str_p)
void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
{
int ori_len = b->data_len;
b->data_len += 3 + len;
b->l_aux += 3 + len;
if (b->m_data < b->data_len) {
b->m_data = b->data_len;
kroundup32(b->m_data);
b->data = (uint8_t*)realloc(b->data, b->m_data);
}
b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
b->data[ori_len + 2] = type;
memcpy(b->data + ori_len + 3, data, len);
}
uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
{
return bam_aux_get(b, tag);
}
#define __skip_tag(s) do { \
int type = toupper(*(s)); \
++(s); \
if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
else (s) += bam_aux_type2size(type); \
} while(0)
uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
uint8_t *s;
int y = tag[0]<<8 | tag[1];
s = bam1_aux(b);
while (s < b->data + b->data_len) {
int x = (int)s[0]<<8 | s[1];
s += 2;
if (x == y) return s;
__skip_tag(s);
}
return 0;
}
// s MUST BE returned by bam_aux_get()
int bam_aux_del(bam1_t *b, uint8_t *s)
{
uint8_t *p, *aux;
aux = bam1_aux(b);
p = s - 2;
__skip_tag(s);
memmove(p, s, b->l_aux - (s - aux));
b->data_len -= s - p;
b->l_aux -= s - p;
return 0;
}
int bam_aux_drop_other(bam1_t *b, uint8_t *s)
{
if (s) {
uint8_t *p, *aux;
aux = bam1_aux(b);
p = s - 2;
__skip_tag(s);
memmove(aux, p, s - p);
b->data_len -= b->l_aux - (s - p);
b->l_aux = s - p;
} else {
b->data_len -= b->l_aux;
b->l_aux = 0;
}
return 0;
}
void bam_init_header_hash(bam_header_t *header)
{
if (header->hash == 0) {
int ret, i;
khiter_t iter;
khash_t(s) *h;
header->hash = h = kh_init(s);
for (i = 0; i < header->n_targets; ++i) {
iter = kh_put(s, h, header->target_name[i], &ret);
kh_value(h, iter) = i;
}
}
}
void bam_destroy_header_hash(bam_header_t *header)
{
if (header->hash)
kh_destroy(s, (khash_t(s)*)header->hash);
}
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
{
khint_t k;
khash_t(s) *h = (khash_t(s)*)header->hash;
k = kh_get(s, h, seq_name);
return k == kh_end(h)? -1 : kh_value(h, k);
}
int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
{
char *s;
int i, l, k, name_end;
khiter_t iter;
khash_t(s) *h;
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
*ref_id = *beg = *end = -1;
name_end = l = strlen(str);
s = (char*)malloc(l+1);
// remove space
for (i = k = 0; i < l; ++i)
if (!isspace(str[i])) s[k++] = str[i];
s[k] = 0; l = k;
// determine the sequence name
for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
if (i >= 0) name_end = i;
if (name_end < l) { // check if this is really the end
int n_hyphen = 0;
for (i = name_end + 1; i < l; ++i) {
if (s[i] == '-') ++n_hyphen;
else if (!isdigit(s[i]) && s[i] != ',') break;
}
if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
s[name_end] = 0;
iter = kh_get(s, h, s);
if (iter == kh_end(h)) { // cannot find the sequence name
iter = kh_get(s, h, str); // try str as the name
if (iter == kh_end(h)) {
if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
free(s); return -1;
} else s[name_end] = ':', name_end = l;
}
} else iter = kh_get(s, h, str);
*ref_id = kh_val(h, iter);
// parse the interval
if (name_end < l) {
for (i = k = name_end + 1; i < l; ++i)
if (s[i] != ',') s[k++] = s[i];
s[k] = 0;
*beg = atoi(s + name_end + 1);
for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
*end = i < k? atoi(s + i + 1) : 1<<29;
if (*beg > 0) --*beg;
} else *beg = 0, *end = 1<<29;
free(s);
return *beg <= *end? 0 : -1;
}
int32_t bam_aux2i(const uint8_t *s)
{
int type;
if (s == 0) return 0;
type = *s++;
if (type == 'c') return (int32_t)*(int8_t*)s;
else if (type == 'C') return (int32_t)*(uint8_t*)s;
else if (type == 's') return (int32_t)*(int16_t*)s;
else if (type == 'S') return (int32_t)*(uint16_t*)s;
else if (type == 'i' || type == 'I') return *(int32_t*)s;
else return 0;
}
float bam_aux2f(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0.0;
if (type == 'f') return *(float*)s;
else return 0.0;
}
double bam_aux2d(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0.0;
if (type == 'd') return *(double*)s;
else return 0.0;
}
char bam_aux2A(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0;
if (type == 'A') return *(char*)s;
else return 0;
}
char *bam_aux2Z(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0;
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
#ifdef _WIN32
double drand48()
{
return (double)rand() / RAND_MAX;
}
#endif
|
